生物科学理论侧重于理论生物学的新概念。它还包括分析和建模方法以及哲学和历史问题。中心主题是：人工生命；关注新方法、现象和解释的生物信息学；仿生建模；复杂性、稳健性和弹性；具身认知；进化生物学；EVO-DEVO；博弈论建模；遗传学；生物学史；语言进化；数学生物学；生命起源；生物学哲学；种群生物学；系统生物学；理论生态学；理论分子生物学；理论神经科学与认知。

The journal "Theory in Biosciences" focuses on new concepts in theoretical biology. It encompasses analytical and modeling methods, as well as philosophical and historical issues. The central themes include: artificial life; new methods, phenomena, and explanations in bioinformatics; biomimetic modeling; complexity, robustness, and resilience; embodied cognition; evolutionary biology; EVO-DEVO; game-theoretic modeling; genetics; history of biology; language evolution; mathematical biology; origin of life; philosophy of biology; population biology; systems biology; theoretical ecology; theoretical molecular biology; theoretical neuroscience and cognition.

《Theory in Biosciences》期刊专注于理论生物学的新概念，涵盖分析与建模方法，以及相关的哲学和历史问题。主要主题包括：人工生命；生物信息学的新方法、现象和解释；仿生建模；复杂性、稳健性和弹性；具身认知；进化生物学；EVO-DEVO；博弈论建模；遗传学；生物学史；语言进化；数学生物学；生命起源；生物学哲学；种群生物学；系统生物学；理论生态学；理论分子生物学；理论神经科学与认知。

Theory in Biosciences

The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named “Prebiotic Chemical Refugia.” Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.

Francisco Prosdocimi

Sávio Torres de Farias

Marco V. José

Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth

前生物化学避难所：原始地球上生物分子形成的多元情景

Abstract Circular codes, which are considered as putative remnants of primaeval comma-free codes, have recently become a focal point of research. These codes constitute a secondary type of genetic code, primarily tasked with detecting and preserving the normal reading frame within protein-coding sequences. The identification of a universal code present across various species has sparked numerous theoretical and experimental inquiries. Among these, the exploration of the class of 216 self-complementary $$C^3$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mi>C</mml:mi> <mml:mn>3</mml:mn> </mml:msup> </mml:math> -codes of maximum size 20 has garnered significant attention. However, the origin of the number 216 lacks a satisfactory explanation, and the mathematical construction of these codes remains elusive. This paper introduces a new software designed to facilitate the construction of self-complementary $$C^3$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mi>C</mml:mi> <mml:mn>3</mml:mn> </mml:msup> </mml:math> -codes (of maximum size). The approach involves a systematic exclusion of codons, guided by two fundamental mathematical theorems. These theorems demonstrate how codons can be automatically excluded from consideration when imposing requirements such as self-complementarity, circularity or maximality. By leveraging these theorems, our software provides a novel and efficient means to construct these intriguing circular codes, shedding light on their mathematical foundations and contributing to a deeper understanding of their biological significance.

Elena Fimmel

Hadi Saleh

Lutz Strüngmann

Forbidden codon combinations in error-detecting circular codes

循环码中禁用的密码子组合在错误检测中的作用

In biology, the concept of "living organism" has traditionally been based on the smallest level of organization comprising all the necessary and essential characteristics of life: the cell. Today, this concept is being challenged by the analysis of ambiguous biological entities, located both below and above the level of the living cell, which exhibit some of the characteristics of living organisms. This situation has given rise to an epistemological pluralism of the concepts of "organism", "individual" and "living", for which no clear and unanimous definition has yet been accepted. The aim of this manuscript is to explore new ideas and perspectives for defining the concept of "living organism", in order to eliminate a certain level of pluralism that could generate confusion, particularly in the pragmatic context of biological research. First, I expose the dualism of the concepts of "organism" and "individual" and suggest a fusion of these concepts in order to eliminate a certain level of pluralism. In doing so, I develop a symbiotic and holistic definition of the concept of "living organism", which includes different structural levels of the organism: molecular, cellular and ecosystems. Second, I present the epistemological problem of the concept of "living", which is closely related to the concepts of "organism" and "individual", by analyzing the list and gradational types of definition. In doing so, I propose a new symbiotic, holistic and gradualist model of the concept of "living organism", using a gradation of several properties of the living applied to the different structural levels of the organism developed previously (molecular, cellular, ecosystems).

Mirco Plante

Theory Biosci

A new symbiotic, holistic and gradualist model proposal for the concept of “living organism”

“生命体”概念的新共生、整体和渐进主义模型提案

The tumor microenvironment constitutes a complex system shaped by the intricate interactions among tumor cells, immune cells, and cytokines. Within this environment, the interplay between immune cells and cytokines is crucial in influencing tumor growth and progression. Despite advancements in clinical tumor immunotherapy, there remains a gap in comprehensive simulations of tumor immune responses, particularly regarding cytokine-driven processes. This study aims to address this gap by investigating the regulatory interactions among tumor cells, immune cells, and cytokines to simulate the complexities of tumor immunotherapy. We develop a comprehensive modeling and computational framework incorporating PD-1 inhibitors and interleukin-10 (IL-10) antibodies. Through detailed mathematical analysis, we elucidate the impact of changes in the immune microenvironment on tumor cells number. Our findings highlight the significant therapeutic effect of anti-PD-1 and IL-10 inhibitors, with increased drug dosage correlating with a reduction in tumor burden. Furthermore, combination therapy demonstrates a marked extension of survival with reduced dosages compared to monotherapy. Based on model simulations, we proposed prognostic predictions by assessing the microenvironmental status before treatment. The findings indicate a promising method for enhancing treatment effectiveness and offering potential advantages to patients receiving tumor immunotherapy.

Zixin Zhang

Xiyin Liang

Jianyong Qin

Jinzhi Lei

Mathematical model of tumor immune microenvironment with application to the combined therapy targeting the PD-1/PD-L1 pathway and IL-10 cytokine antibody

肿瘤免疫微环境数学模型及其在靶向PD-1/PD-L1通路和IL-10细胞因子抗体联合治疗中的应用

The conflict between individual and collective interests makes fostering cooperation in human societies a challenging task, requiring drastic measures such as the establishment of sanctioning institutions. These institutions are costly because they have to be maintained regardless of the presence or absence of offenders. Here, we revisit some improvements to the standard N-person prisoner's dilemma formulation with institutional punishment in a well-mixed population, namely the elimination of overpunishment, the requirement of a minimum number of contributors to establish the sanctioning institution, and the sharing of its maintenance costs once this minimum number is reached. In addition, we focus on large groups or communities for which sanctioning institutions are ubiquitous. Using the replicator equation framework for an infinite population, we find that by sufficiently fining players who fail to contribute either to the public good or to the sanctioning institution, a population of contributors immune to invasion by these free riders can be established, provided that the contributors are sufficiently numerous. In a finite population, we use finite-size scaling to show that, for some parameter settings, demographic noise helps to fixate the strategy that contributes to the public good but not to the sanctioning institution even for infinitely large populations when, somewhat counterintuitively, its proportion in the initial population vanishes with a small power of the population size.

Abbreviation	Theory Biosci.
Journal Impact	1.36
Quartiles(Global)	MATHEMATICAL & COMPUTATIONAL BIOLOGY(Q4)

ISSN	1431-7613, 1611-7530
h-index	41

Publication Information	Publisher: Springer Verlag，Publishing cycle: Tri-annual，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 1997，Proportion of original research papers: 95.45%，Self Citation Rate:0.00%， Gold OA Rate: 36.36%
Average review cycle	网友分享经验：>12周，或约稿
Average recruitment ratio	网友分享经验：容易

Theory in Biosciences

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Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth

Forbidden codon combinations in error-detecting circular codes

A new symbiotic, holistic and gradualist model proposal for the concept of “living organism”

Mathematical model of tumor immune microenvironment with application to the combined therapy targeting the PD-1/PD-L1 pathway and IL-10 cytokine antibody

Revisiting institutional punishment in the N-person prisoner’s dilemma

Forbidden codon combinations in error-detecting circular codes

A new symbiotic, holistic and gradualist model proposal for the concept of “living organism”

Mathematical model of tumor immune microenvironment with application to the combined therapy targeting the PD-1/PD-L1 pathway and IL-10 cytokine antibody

Editorial

Revisiting institutional punishment in the N-person prisoner’s dilemma